Biology subjects

Alam, K.

Publications and source records attributed to Alam, K..

4 recordsLinked to original sources

bioRxiv2026

Distinct Programs of Tissue Adaptation Shape Vitreous CD4+ and CD8+ T-cell States in Chronic Uveitis

Tissue-resident memory (TRM) T-cells are increasingly recognized as key mediators of chronic autoimmune inflammation, yet their organization and functional adaptation within the eye remain poorly understood. We investigated paired vitreous body biopsies and peripheral blood T cells from patients with chronic posterior segment uveitis using multiparameter flow cytometry, antigen-specific stimulation assays, single-cell RNA sequencing, and T-cell receptor sequencing to define the intraocular tissue-adaptive immune states. Vitreous T cells were phenotypically, transcriptionally, and clonally distinct from their circulating counterparts and enriched for canonical TRM markers. However, tissue adaptation differed substantially between CD4+ and CD8+ lineages. Vitreous CD4+ T cells segregated into clonally expanded tissue-adaptive states characterized by greater CXCR6 expression, enhanced antigen-specific cytokine responses, and well-defined transcriptional profiles. In contrast, vitreous CD8+ T cells expressed higher levels of the retention-associated markers CD103 and CD49a yet maintained greater clonal and phenotypic continuity with peripheral blood T cells. Both vitreous CD4+ and CD8+ subsets exhibited a restrained effector profile associated with tissue-adaptive transcriptional programs. Our data reveal that CD4+ and CD8+ T cells in chronic uveitis assume distinct states in the vitreous microenvironment, such that the intraocular immune response relies on both localized tissue retention and active adaptation to the inflammatory niche.

immunology↗

bioRxiv2023

Cryptic connectivity between hyporheic and riparian zones via winged aquatic insects revealed by DNA barcoding

How subsurface hyporheic zone (HZ) of rivers is connected to riparian zones remains largely unknown. We collected benthic macroinvertebrates and adult aquatic insects for six years, including those at 30-cm depth in the HZ to identify insect taxa having a high level of habitat affinity for HZ (HZ taxa). Adults of HZ taxa were identified with the aid of CO1 gene barcoding, and the relative abundance of HZ taxa in the riparian zone was quantified. In addition to the previously known stonefly Alloperla ishikariana, three species of stonefly Leuctridae and one caddisfly species of Philopotamidae were identified as HZ taxa. At the annual scale, HZ taxa accounted for approximately 38% of the total aquatic insects in the family of stoneflies (Plecoptera), caddisflies (Trichoptera), and mayflies (Ephemeroptera) in abundance and 26% of biomass, with their seasonal peaks in early spring and mid-summer (60% in abundance and 47% in biomass). Few individuals of HZ taxa were found in benthic samples (<0.1%), and hyporheic samples quantified more but erroneously estimated relative abundances of adult HZ taxa, with Leuctridae and Philopotamidae being substantially underrepresented relative to their adult abundance. Cryptic biological connectivity between subsurface and riparian zones via winged HZ-taxa adults is substantial. DNA-based species identification combined with community surveys of adult HZ-taxa complementarily used with benthic data can substantially improve the effectiveness of biomonitoring programs and outcomes of habitat conservation based on more complete picture of ecosystem health.

ecology↗

bioRxiv2019

Rapid, Low-Cost Detection of Water Contaminants Using Regulated In Vitro Transcription

Synthetic biology has enabled the development of powerful nucleic acid diagnostic technologies for detecting pathogens and human health biomarkers. Here we expand the reach of synthetic biology-enabled diagnostics by developing a cell-free biosensing platform that uses RNA output sensors activated by ligand induction (ROSALIND) to detect harmful contaminants in aqueous samples. ROSALIND consists of three programmable components: highly-processive RNA polymerases, allosteric transcription factors, and synthetic DNA transcription templates. Together, these components allosterically regulate the in vitro transcription of a fluorescence-activating RNA aptamer: in the absence of a target compound, transcription is blocked, while in its presence a fluorescent signal is produced. We demonstrate that ROSALIND can be configured to detect a range of water contaminants, including antibiotics, toxic small molecules, and metals. Our cell-free biosensing platform, which can be freeze-dried for field deployment, creates a new capability for point-of-use monitoring of molecular species to address growing global crises in water quality and human health.

synthetic biology↗

bioRxiv2018

Detection of Mycobacterium leprae DNA in soil; Multiple needles in the haystack?

BackgroundLeprosy is an infectious disease caused by Mycobacterium leprae and Mycobacterium lepromatosis affecting the skin and nerves. Despite decades of availability of adequate treatment, transmission is unabated and routes of transmission are not completely understood. Notwithstanding the general assumption that untreated M. leprae infected humans represent the major source of transmission, scarce reports indicate that environmental specimens could play a role as a reservoir as well.\n\nMethodologyIn order to identify patterns of bacterial transmission, this study investigated whether M. leprae DNA is present in soil of regions where leprosy is endemic or areas with possible animal reservoirs (armadillos and red squirrels). Soil samples were collected in Bangladesh, Suriname and the British Isles. The presence of M. leprae DNA was determined by RLEP PCR and M. leprae SNP types were further identified by Sanger sequencing of loci 1-3.\n\nResultsM. leprae DNA was identified in soil samples from environments inhabited by leprosy patients (Bangladesh), armadillos (Suriname) and the lepromatous Eurasian red squirrels (British Isles). In Bangladesh SNP type 1 was detected, Suriname soil contained SNP type 1 or 2, whilst SNP typing was not feasible for the British samples.\n\nConclusionsIt is conceivable that, besides humans and animals, environmental reservoirs may play a role in transmission. Frequent, intense contact with multibacillary leprosy patients poses the highest risk of transmission, and even though the risk of environmental contamination is low, it may offer a possible explanation for the occurrence of leprosy in individuals in areas without any reported human leprosy.

microbiology↗